Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xaa Working: n-1-16.cluster.ucsf.bkslab.org:/scratch/xiaobo/372095/xaa-8058088.1 Result: /scratch/xiaobo/372095/xaa-8058088.1 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa Task: /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xaa mkdir: created directory `/scratch/xiaobo/372095' mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1' /scratch/xiaobo/372095/xaa-8058088.1 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers! STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working' mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/protonate' Storing results in /scratch/xiaobo/372095/xaa-8058088.1/finished Working in /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 /scratch/xiaobo/372095/xaa-8058088.1/working/protonate /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Using inputs as protomers/tautomers. No processing done 446 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/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Bulk generating 3D conformations all protomers in /scratch/xiaobo/372095/xaa-8058088.1/working/3D mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/372095/xaa-8058088.1/working/protonate/xaa-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 ZINC001617454137 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building' mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001617454137 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/1 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@](C)CC1) `ZINC001617454137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617454137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617454137 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/2 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1) `ZINC001617454137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617454137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617454137 none C#CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/3 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/3' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1) `ZINC001617454137.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617454137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617454137 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001617454137 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/finished' Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/2.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 Building ZINC001617454137 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001617454137 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 1) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@](C)CC1) `ZINC001617454137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617454137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617454137 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 2) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1) `ZINC001617454137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617454137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617454137 none C#CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 3) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1) `ZINC001617454137.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617454137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617454137 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001617454137 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/2.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 Building ZINC001617454137 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001617454137 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 1) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@](C)CC1) `ZINC001617454137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617454137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617454137 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 2) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1) `ZINC001617454137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617454137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617454137 none C#CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 3) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1) `ZINC001617454137.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617454137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617454137 none C#CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001617454137 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/2.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617454137 Building ZINC001617870187 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617870187 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/4 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(C#N)cs1) `ZINC001617870187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617870187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001617870187 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(C#N)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/5 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(C#N)cs1) `ZINC001617870187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617870187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001617870187 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(C#N)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001617870187 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 Building ZINC001617870187 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617870187 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 4) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(C#N)cs1) `ZINC001617870187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617870187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001617870187 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc(C#N)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 5) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(C#N)cs1) `ZINC001617870187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617870187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001617870187 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc(C#N)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001617870187 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001617870187 Building ZINC001621514774 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001621514774 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/6 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCOC1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001621514774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001621514774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621514774 none CC(C)(C)OC(=O)NCCCOC1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 37, 16, 16, 7, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 27, 16, 16, 16, 16, 7, 7, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/7 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCOC1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001621514774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001621514774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621514774 none CC(C)(C)OC(=O)NCCCOC1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 30, 45, 20, 20, 13, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 30, 20, 20, 20, 20, 13, 13, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001621514774 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 Building ZINC001621514774 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001621514774 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 6) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CC(C)(C)OC(=O)NCCCOC1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001621514774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001621514774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621514774 none CC(C)(C)OC(=O)NCCCOC1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 37, 16, 16, 7, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 27, 16, 16, 16, 16, 7, 7, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 7) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CC(C)(C)OC(=O)NCCCOC1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001621514774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001621514774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621514774 none CC(C)(C)OC(=O)NCCCOC1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 30, 45, 20, 20, 13, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 30, 20, 20, 20, 20, 13, 13, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001621514774 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001621514774 Building ZINC001623897514 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623897514 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/8 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001623897514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623897514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001623897514 none CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 13, 16, 22, 23, 23, 23, 23, 28, 28, 28, 28, 28, 23, 23, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 23, 23, 23, 23, 28, 28, 28, 28, 28, 23, 23, 23, 23, 2, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/9 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001623897514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623897514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001623897514 none CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 13, 16, 22, 24, 24, 24, 24, 28, 28, 28, 28, 28, 24, 24, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 24, 24, 24, 24, 28, 28, 28, 28, 28, 24, 24, 24, 24, 2, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001623897514 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 Building ZINC001623897514 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623897514 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 8) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001623897514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623897514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001623897514 none CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 13, 16, 22, 23, 23, 23, 23, 28, 28, 28, 28, 28, 23, 23, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 23, 23, 23, 23, 28, 28, 28, 28, 28, 23, 23, 23, 23, 2, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 9) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001623897514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623897514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001623897514 none CC(C)(CC(=O)N1CCN(c2ccccc2)CC1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 13, 16, 22, 24, 24, 24, 24, 28, 28, 28, 28, 28, 24, 24, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 24, 24, 24, 24, 28, 28, 28, 28, 28, 24, 24, 24, 24, 2, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001623897514 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623897514 Building ZINC001623931446 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623931446 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/10 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1S(=O)(=O)N1CCCC1) `ZINC001623931446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623931446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001623931446 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1S(=O)(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 6, 6, 3, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 9, 10, 10, 10, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 6, 6, 3, 7, 7, 10, 10, 10, 10, 6, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/11 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1S(=O)(=O)N1CCCC1) `ZINC001623931446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623931446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001623931446 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1S(=O)(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 7, 5, 7, 7, 3, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 3, 7, 7, 10, 10, 10, 10, 7, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001623931446 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 Building ZINC001623931446 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623931446 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 10) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1S(=O)(=O)N1CCCC1) `ZINC001623931446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623931446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001623931446 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1S(=O)(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 4, 4, 6, 6, 3, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 9, 10, 10, 10, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 6, 6, 3, 7, 7, 10, 10, 10, 10, 6, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 11) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1S(=O)(=O)N1CCCC1) `ZINC001623931446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623931446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001623931446 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1S(=O)(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 7, 5, 7, 7, 3, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 3, 7, 7, 10, 10, 10, 10, 7, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001623931446 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001623931446 Building ZINC001624328831 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624328831 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/12 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br) `ZINC001624328831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624328831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001624328831 none Cc1ccc(C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 18, 17, 9, 17, 16, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 16, 17, 51, 9, 9, 3, 5, 5, 8, 8, 8, 8, 26] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/13 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br) `ZINC001624328831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624328831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001624328831 none Cc1ccc(C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 24, 24, 17, 15, 10, 15, 15, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 16, 16, 48, 10, 10, 2, 6, 6, 8, 8, 8, 8, 24] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001624328831 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 Building ZINC001624328831 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624328831 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 12) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1ccc(C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br) `ZINC001624328831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624328831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001624328831 none Cc1ccc(C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 18, 17, 9, 17, 16, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 16, 17, 51, 9, 9, 3, 5, 5, 8, 8, 8, 8, 26] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 13) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1ccc(C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br) `ZINC001624328831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624328831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001624328831 none Cc1ccc(C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 24, 24, 17, 15, 10, 15, 15, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 16, 16, 48, 10, 10, 2, 6, 6, 8, 8, 8, 8, 24] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001624328831 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328831 Building ZINC001624328832 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624328832 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/14 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br) `ZINC001624328832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624328832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001624328832 none Cc1ccc(C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 24, 24, 17, 15, 10, 15, 15, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 16, 16, 48, 10, 10, 2, 6, 6, 8, 8, 8, 8, 24] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/15 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br) `ZINC001624328832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624328832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001624328832 none Cc1ccc(C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 18, 17, 9, 17, 16, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 9, 9, 8, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 17, 16, 51, 9, 9, 3, 6, 6, 9, 9, 9, 9, 26] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001624328832 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 Building ZINC001624328832 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624328832 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 14) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1ccc(C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br) `ZINC001624328832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624328832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001624328832 none Cc1ccc(C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 24, 24, 17, 15, 10, 15, 15, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 16, 16, 48, 10, 10, 2, 6, 6, 8, 8, 8, 8, 24] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 15) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1ccc(C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br) `ZINC001624328832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624328832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001624328832 none Cc1ccc(C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 18, 17, 9, 17, 16, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 9, 9, 8, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 17, 16, 51, 9, 9, 3, 6, 6, 9, 9, 9, 9, 26] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001624328832 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624328832 Building ZINC001624346468 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624346468 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/16 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1cc(Br)ccc1F)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001624346468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624346468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624346468 none O=C(NC[C@H](CO)Cc1cc(Br)ccc1F)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 11, 11, 13, 11, 17, 27, 27, 27, 21, 27, 27, 27, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 2, 5, 5, 13, 13, 39, 17, 17, 27, 17, 27, 5, 5, 7, 7, 7, 7] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 194 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/17 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1cc(Br)ccc1F)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001624346468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624346468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624346468 none O=C(NC[C@H](CO)Cc1cc(Br)ccc1F)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 7, 7, 10, 7, 14, 24, 24, 24, 18, 24, 24, 24, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 1, 4, 4, 10, 10, 30, 14, 14, 24, 18, 24, 4, 4, 7, 7, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 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: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001624346468 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 Building ZINC001624346468 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624346468 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 16) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(NC[C@H](CO)Cc1cc(Br)ccc1F)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001624346468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624346468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624346468 none O=C(NC[C@H](CO)Cc1cc(Br)ccc1F)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 11, 11, 13, 11, 17, 27, 27, 27, 21, 27, 27, 27, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 2, 5, 5, 13, 13, 39, 17, 17, 27, 17, 27, 5, 5, 7, 7, 7, 7] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 194 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 17) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(NC[C@H](CO)Cc1cc(Br)ccc1F)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001624346468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624346468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624346468 none O=C(NC[C@H](CO)Cc1cc(Br)ccc1F)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 7, 7, 10, 7, 14, 24, 24, 24, 18, 24, 24, 24, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 1, 4, 4, 10, 10, 30, 14, 14, 24, 18, 24, 4, 4, 7, 7, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 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: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001624346468 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346468 Building ZINC001624346469 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624346469 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/18 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1cc(Br)ccc1F)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001624346469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624346469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624346469 none O=C(NC[C@@H](CO)Cc1cc(Br)ccc1F)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 8, 8, 11, 8, 15, 25, 25, 25, 19, 25, 25, 25, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 1, 4, 4, 11, 11, 33, 15, 15, 25, 15, 25, 3, 3, 6, 6, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/19 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1cc(Br)ccc1F)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001624346469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624346469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624346469 none O=C(NC[C@@H](CO)Cc1cc(Br)ccc1F)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 11, 11, 13, 11, 16, 26, 26, 26, 20, 26, 26, 26, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 2, 5, 5, 13, 13, 39, 16, 16, 26, 16, 26, 5, 5, 8, 8, 8, 8] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001624346469 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 Building ZINC001624346469 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624346469 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 18) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(NC[C@@H](CO)Cc1cc(Br)ccc1F)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001624346469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624346469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624346469 none O=C(NC[C@@H](CO)Cc1cc(Br)ccc1F)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 8, 8, 11, 8, 15, 25, 25, 25, 19, 25, 25, 25, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 1, 4, 4, 11, 11, 33, 15, 15, 25, 15, 25, 3, 3, 6, 6, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 19) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(NC[C@@H](CO)Cc1cc(Br)ccc1F)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001624346469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624346469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624346469 none O=C(NC[C@@H](CO)Cc1cc(Br)ccc1F)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 11, 11, 13, 11, 16, 26, 26, 26, 20, 26, 26, 26, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 2, 5, 5, 13, 13, 39, 16, 16, 26, 16, 26, 5, 5, 8, 8, 8, 8] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001624346469 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624346469 Building ZINC001624379576 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624379576 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/20 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#Cc1c(N)n(c2ccc(F)cc2)nc1CCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624379576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624379576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001624379576 none N#Cc1c(N)n(c2ccc(F)cc2)nc1CCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 40, 40, 22, 22, 40, 40, 22, 12, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 40, 40, 40, 40, 12, 12, 9, 9, 8, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/21 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#Cc1c(N)n(c2ccc(F)cc2)nc1CCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624379576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624379576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001624379576 none N#Cc1c(N)n(c2ccc(F)cc2)nc1CCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 37, 37, 23, 23, 37, 37, 23, 12, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 37, 37, 37, 37, 12, 12, 9, 9, 8, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001624379576 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 Building ZINC001624379576 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624379576 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 20) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: N#Cc1c(N)n(c2ccc(F)cc2)nc1CCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624379576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624379576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001624379576 none N#Cc1c(N)n(c2ccc(F)cc2)nc1CCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 40, 40, 22, 22, 40, 40, 22, 12, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 40, 40, 40, 40, 12, 12, 9, 9, 8, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 21) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: N#Cc1c(N)n(c2ccc(F)cc2)nc1CCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624379576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624379576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001624379576 none N#Cc1c(N)n(c2ccc(F)cc2)nc1CCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 37, 37, 23, 23, 37, 37, 23, 12, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 37, 37, 37, 37, 12, 12, 9, 9, 8, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001624379576 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001624379576 Building ZINC001625763202 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625763202 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/22 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CNC(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)cc1F) `ZINC001625763202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625763202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001625763202 none Cc1ccc(CNC(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 4, 4, 3, 4, 3, 3, 3, 2, 1, 3, 1, 1, 1, 3, 3, 6, 6, 3, 3, 6, 6, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 20, 20, 4, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 3, 3, 3, 3, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/23 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CNC(=O)C2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)cc1F) `ZINC001625763202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625763202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001625763202 none Cc1ccc(CNC(=O)C2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 3, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 3, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 4, 3, 3, 3, 3, 30] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001625763202 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 Building ZINC001625763202 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625763202 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 22) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1ccc(CNC(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)cc1F) `ZINC001625763202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625763202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001625763202 none Cc1ccc(CNC(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 4, 4, 3, 4, 3, 3, 3, 2, 1, 3, 1, 1, 1, 3, 3, 6, 6, 3, 3, 6, 6, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 20, 20, 4, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 3, 3, 3, 3, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 23) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1ccc(CNC(=O)C2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)cc1F) `ZINC001625763202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625763202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001625763202 none Cc1ccc(CNC(=O)C2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 3, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 3, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 4, 3, 3, 3, 3, 30] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001625763202 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001625763202 Building ZINC001626565397 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626565397 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/24 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(N2CCOCC2)c(Br)cn1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001626565397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626565397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001626565397 none O=C(Nc1cc(N2CCOCC2)c(Br)cn1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 12, 17, 17, 17, 17, 17, 7, 7, 7, 7, 1, 1, 1, 7, 7, 11, 11, 7, 11, 11, 11, 4, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/25 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(N2CCOCC2)c(Br)cn1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001626565397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626565397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001626565397 none O=C(Nc1cc(N2CCOCC2)c(Br)cn1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 12, 17, 17, 17, 17, 17, 7, 7, 7, 7, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 4, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001626565397 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 Building ZINC001626565397 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626565397 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 24) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(N2CCOCC2)c(Br)cn1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001626565397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626565397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001626565397 none O=C(Nc1cc(N2CCOCC2)c(Br)cn1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 12, 17, 17, 17, 17, 17, 7, 7, 7, 7, 1, 1, 1, 7, 7, 11, 11, 7, 11, 11, 11, 4, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 25) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(N2CCOCC2)c(Br)cn1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001626565397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626565397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001626565397 none O=C(Nc1cc(N2CCOCC2)c(Br)cn1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 12, 17, 17, 17, 17, 17, 7, 7, 7, 7, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 4, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001626565397 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001626565397 Building ZINC001627502975 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627502975 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/26 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1) `ZINC001627502975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627502975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001627502975 none O=C(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 1, 7, 7, 24, 24, 24, 24, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 1, 1, 7, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 12, 34, 46, 13, 11, 35, 47, 22, 36, 38, 37] set([0, 1, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/27 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1) `ZINC001627502975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627502975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001627502975 none O=C(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 4, 4, 6, 6, 4, 4, 6, 6, 4, 14, 14, 37, 37, 37, 37, 37, 37, 37, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 4, 4, 14, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001627502975 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 Building ZINC001627502975 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627502975 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 26) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1) `ZINC001627502975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627502975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001627502975 none O=C(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 1, 7, 7, 24, 24, 24, 24, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 1, 1, 7, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 12, 34, 46, 13, 11, 35, 47, 22, 36, 38, 37] set([0, 1, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 27) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1) `ZINC001627502975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627502975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001627502975 none O=C(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 4, 4, 6, 6, 4, 4, 6, 6, 4, 14, 14, 37, 37, 37, 37, 37, 37, 37, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 4, 4, 14, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001627502975 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502975 Building ZINC001627502976 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627502976 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/28 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1) `ZINC001627502976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627502976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001627502976 none O=C(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 4, 15, 15, 38, 38, 38, 38, 38, 38, 38, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 4, 4, 15, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/29 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1) `ZINC001627502976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627502976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001627502976 none O=C(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 1, 7, 7, 26, 26, 26, 26, 26, 26, 26, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 1, 1, 7, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 12, 34, 46, 13, 11, 35, 47, 22, 36, 38, 37] set([0, 1, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001627502976 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 Building ZINC001627502976 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627502976 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 28) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1) `ZINC001627502976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627502976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001627502976 none O=C(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 4, 15, 15, 38, 38, 38, 38, 38, 38, 38, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 4, 4, 15, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 29) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1) `ZINC001627502976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627502976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001627502976 none O=C(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)NCc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 1, 7, 7, 26, 26, 26, 26, 26, 26, 26, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 1, 1, 7, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 12, 34, 46, 13, 11, 35, 47, 22, 36, 38, 37] set([0, 1, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001627502976 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627502976 Building ZINC001627569140 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627569140 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/30 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H](C(F)(F)F)N(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)C(F)(F)F) `ZINC001627569140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627569140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001627569140 none O=C(N[C@@H]1CC[C@@H](C(F)(F)F)N(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 2, 10, 1, 1, 1, 9, 9, 14, 14, 9, 9, 14, 14, 12, 20, 20, 20, 20, 20, 12, 12, 12, 12, 9, 9, 14, 14, 14, 14, 12, 12] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/31 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H](C(F)(F)F)N(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)C(F)(F)F) `ZINC001627569140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627569140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001627569140 none O=C(N[C@@H]1CC[C@@H](C(F)(F)F)N(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 9, 9, 13, 13, 9, 9, 13, 13, 9, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001627569140 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 Building ZINC001627569140 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627569140 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 30) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N[C@@H]1CC[C@@H](C(F)(F)F)N(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)C(F)(F)F) `ZINC001627569140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627569140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001627569140 none O=C(N[C@@H]1CC[C@@H](C(F)(F)F)N(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 2, 10, 1, 1, 1, 9, 9, 14, 14, 9, 9, 14, 14, 12, 20, 20, 20, 20, 20, 12, 12, 12, 12, 9, 9, 14, 14, 14, 14, 12, 12] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 31) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N[C@@H]1CC[C@@H](C(F)(F)F)N(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)C(F)(F)F) `ZINC001627569140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627569140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001627569140 none O=C(N[C@@H]1CC[C@@H](C(F)(F)F)N(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 9, 9, 13, 13, 9, 9, 13, 13, 9, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001627569140 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627569140 Building ZINC001627995006 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627995006 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/32 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1OC) `ZINC001627995006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627995006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001627995006 none COc1ccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 26, 26, 26, 19, 9, 9, 9, 9, 9, 5, 3, 1, 3, 1, 1, 1, 5, 5, 7, 7, 5, 5, 7, 7, 26, 26, 27, 26, 26, 27, 28, 28, 28, 26, 26, 19, 19, 9, 9, 5, 5, 5, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/33 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1OC) `ZINC001627995006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627995006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001627995006 none COc1ccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 24, 24, 24, 18, 9, 9, 9, 9, 9, 5, 3, 1, 3, 1, 1, 1, 5, 5, 7, 7, 5, 5, 7, 7, 24, 24, 25, 24, 24, 25, 26, 26, 26, 24, 24, 18, 18, 9, 9, 5, 5, 5, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001627995006 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 Building ZINC001627995006 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627995006 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 32) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COc1ccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1OC) `ZINC001627995006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627995006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001627995006 none COc1ccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 26, 26, 26, 19, 9, 9, 9, 9, 9, 5, 3, 1, 3, 1, 1, 1, 5, 5, 7, 7, 5, 5, 7, 7, 26, 26, 27, 26, 26, 27, 28, 28, 28, 26, 26, 19, 19, 9, 9, 5, 5, 5, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 33) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COc1ccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1OC) `ZINC001627995006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627995006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001627995006 none COc1ccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 24, 24, 24, 18, 9, 9, 9, 9, 9, 5, 3, 1, 3, 1, 1, 1, 5, 5, 7, 7, 5, 5, 7, 7, 24, 24, 25, 24, 24, 25, 26, 26, 26, 24, 24, 18, 18, 9, 9, 5, 5, 5, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001627995006 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001627995006 Building ZINC001628197619 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628197619 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/34 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C(=O)C(F)(F)c2cc(NC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)ccc21) `ZINC001628197619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628197619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628197619 none CCOC(=O)CN1C(=O)C(F)(F)c2cc(NC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 21, 19, 16, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 9, 9, 8, 24, 24, 24, 24, 24, 16, 16, 9, 3, 7, 7, 10, 10, 10, 10, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/35 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN1C(=O)C(F)(F)c2cc(NC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)ccc21) `ZINC001628197619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628197619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628197619 none CCOC(=O)CN1C(=O)C(F)(F)c2cc(NC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 20, 16, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 8, 25, 25, 25, 25, 25, 16, 16, 10, 3, 8, 8, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001628197619 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 Building ZINC001628197619 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628197619 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 34) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CCOC(=O)CN1C(=O)C(F)(F)c2cc(NC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)ccc21) `ZINC001628197619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628197619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628197619 none CCOC(=O)CN1C(=O)C(F)(F)c2cc(NC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 21, 19, 16, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 9, 9, 8, 24, 24, 24, 24, 24, 16, 16, 9, 3, 7, 7, 10, 10, 10, 10, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 35) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CCOC(=O)CN1C(=O)C(F)(F)c2cc(NC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)ccc21) `ZINC001628197619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628197619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628197619 none CCOC(=O)CN1C(=O)C(F)(F)c2cc(NC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 20, 16, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 8, 25, 25, 25, 25, 25, 16, 16, 10, 3, 8, 8, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001628197619 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628197619 Building ZINC001628522851 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628522851 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/36 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001628522851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628522851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001628522851 none COCCN(C(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 16, 8, 2, 8, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 6, 6, 5, 5, 6, 6, 2, 2, 27, 27, 27, 25, 25, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 5, 5, 6, 6, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 155 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/37 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001628522851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628522851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001628522851 none COCCN(C(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 2, 7, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 2, 2, 26, 26, 26, 26, 26, 15, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 154 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001628522851 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 Building ZINC001628522851 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628522851 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 36) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COCCN(C(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001628522851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628522851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001628522851 none COCCN(C(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 16, 8, 2, 8, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 6, 6, 5, 5, 6, 6, 2, 2, 27, 27, 27, 25, 25, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 5, 5, 6, 6, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 155 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 37) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COCCN(C(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001628522851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628522851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001628522851 none COCCN(C(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 2, 7, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 2, 2, 26, 26, 26, 26, 26, 15, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 154 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001628522851 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628522851 Building ZINC001628900923 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628900923 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/38 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#C[C@@H](c1ccc(F)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001628900923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628900923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001628900923 none N#C[C@@H](c1ccc(F)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 7, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 32, 32, 34, 34, 32, 34, 34, 34, 15, 15, 15, 6, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 34, 34, 34, 34, 15, 15, 15, 15, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/39 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#C[C@@H](c1ccc(F)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001628900923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628900923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001628900923 none N#C[C@@H](c1ccc(F)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 7, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 13, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 13, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 31, 31, 31, 31, 13, 13, 13, 13, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001628900923 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 Building ZINC001628900923 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628900923 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 38) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: N#C[C@@H](c1ccc(F)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001628900923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628900923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001628900923 none N#C[C@@H](c1ccc(F)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 7, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 32, 32, 34, 34, 32, 34, 34, 34, 15, 15, 15, 6, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 34, 34, 34, 34, 15, 15, 15, 15, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 39) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: N#C[C@@H](c1ccc(F)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001628900923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628900923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001628900923 none N#C[C@@H](c1ccc(F)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 7, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 13, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 13, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 31, 31, 31, 31, 13, 13, 13, 13, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001628900923 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900923 Building ZINC001628900924 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628900924 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/40 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#C[C@H](c1ccc(F)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001628900924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628900924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001628900924 none N#C[C@H](c1ccc(F)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 7, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 15, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 33, 33, 33, 33, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/41 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#C[C@H](c1ccc(F)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001628900924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628900924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001628900924 none N#C[C@H](c1ccc(F)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 7, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 13, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 29, 29, 29, 29, 13, 13, 13, 13, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001628900924 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 Building ZINC001628900924 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628900924 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 40) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: N#C[C@H](c1ccc(F)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001628900924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628900924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001628900924 none N#C[C@H](c1ccc(F)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 7, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 15, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 33, 33, 33, 33, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 41) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: N#C[C@H](c1ccc(F)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001628900924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628900924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001628900924 none N#C[C@H](c1ccc(F)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 7, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 13, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 29, 29, 29, 29, 13, 13, 13, 13, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001628900924 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001628900924 Building ZINC001629715159 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629715159 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/42 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)CCOc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001629715159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629715159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001629715159 none CS(=O)(=O)CCOc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 21, 13, 7, 7, 7, 4, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 25, 25, 25, 22, 22, 21, 21, 7, 6, 7, 4, 9, 9, 14, 14, 14, 14] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/43 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)CCOc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001629715159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629715159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001629715159 none CS(=O)(=O)CCOc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 27, 27, 23, 14, 7, 7, 7, 6, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 8, 8, 11, 11, 8, 8, 11, 11, 27, 27, 27, 24, 24, 23, 23, 7, 7, 7, 4, 8, 8, 11, 11, 11, 11] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001629715159 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 Building ZINC001629715159 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629715159 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 42) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CS(=O)(=O)CCOc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001629715159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629715159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001629715159 none CS(=O)(=O)CCOc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 21, 13, 7, 7, 7, 4, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 25, 25, 25, 22, 22, 21, 21, 7, 6, 7, 4, 9, 9, 14, 14, 14, 14] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 43) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CS(=O)(=O)CCOc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001629715159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629715159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001629715159 none CS(=O)(=O)CCOc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 27, 27, 23, 14, 7, 7, 7, 6, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 8, 8, 11, 11, 8, 8, 11, 11, 27, 27, 27, 24, 24, 23, 23, 7, 7, 7, 4, 8, 8, 11, 11, 11, 11] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001629715159 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001629715159 Building ZINC001631576127 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631576127 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/44 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(S(=O)(=O)N3CCCCC3)ccc21)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001631576127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631576127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001631576127 none O=C(N1CCc2cc(S(=O)(=O)N3CCCCC3)ccc21)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 4, 4, 4, 4, 19, 19, 19, 26, 26, 26, 26, 21, 4, 4, 4, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/45 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(S(=O)(=O)N3CCCCC3)ccc21)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001631576127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631576127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001631576127 none O=C(N1CCc2cc(S(=O)(=O)N3CCCCC3)ccc21)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 3, 5, 5, 5, 5, 5, 5, 19, 19, 19, 26, 26, 26, 26, 20, 5, 5, 5, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001631576127 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 Building ZINC001631576127 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631576127 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 44) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N1CCc2cc(S(=O)(=O)N3CCCCC3)ccc21)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001631576127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631576127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001631576127 none O=C(N1CCc2cc(S(=O)(=O)N3CCCCC3)ccc21)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 4, 4, 4, 4, 19, 19, 19, 26, 26, 26, 26, 21, 4, 4, 4, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 45) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N1CCc2cc(S(=O)(=O)N3CCCCC3)ccc21)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001631576127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631576127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001631576127 none O=C(N1CCc2cc(S(=O)(=O)N3CCCCC3)ccc21)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 3, 5, 5, 5, 5, 5, 5, 19, 19, 19, 26, 26, 26, 26, 20, 5, 5, 5, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001631576127 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631576127 Building ZINC001631747513 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631747513 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/46 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001631747513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631747513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001631747513 none COc1ccc(S(=O)(=O)C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 8, 8, 8, 4, 8, 8, 14, 14, 14, 16, 16, 16, 8, 3, 3, 1, 3, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 12, 12, 12, 8, 8, 8, 3, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/47 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001631747513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631747513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001631747513 none COc1ccc(S(=O)(=O)C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 8, 8, 8, 6, 8, 8, 14, 14, 14, 16, 16, 16, 8, 3, 3, 1, 3, 1, 1, 1, 7, 7, 11, 11, 7, 7, 11, 11, 12, 12, 12, 8, 8, 8, 3, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001631747513 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 Building ZINC001631747513 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631747513 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 46) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COc1ccc(S(=O)(=O)C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001631747513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631747513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001631747513 none COc1ccc(S(=O)(=O)C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 8, 8, 8, 4, 8, 8, 14, 14, 14, 16, 16, 16, 8, 3, 3, 1, 3, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 12, 12, 12, 8, 8, 8, 3, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 47) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COc1ccc(S(=O)(=O)C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001631747513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631747513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001631747513 none COc1ccc(S(=O)(=O)C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 8, 8, 8, 6, 8, 8, 14, 14, 14, 16, 16, 16, 8, 3, 3, 1, 3, 1, 1, 1, 7, 7, 11, 11, 7, 7, 11, 11, 12, 12, 12, 8, 8, 8, 3, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001631747513 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631747513 Building ZINC001631917933 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631917933 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/48 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(F)cc1F) `ZINC001631917933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631917933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001631917933 none CCCS(=O)(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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: [28, 25, 14, 12, 14, 14, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 7, 7, 10, 10, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 25, 25, 12, 4, 3, 7, 7, 10, 10, 10, 10, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/49 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(F)cc1F) `ZINC001631917933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631917933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001631917933 none CCCS(=O)(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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: [29, 27, 14, 12, 14, 14, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 27, 27, 12, 4, 3, 7, 7, 10, 10, 10, 10, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001631917933 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 Building ZINC001631917933 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631917933 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 48) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CCCS(=O)(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(F)cc1F) `ZINC001631917933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631917933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001631917933 none CCCS(=O)(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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: [28, 25, 14, 12, 14, 14, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 7, 7, 10, 10, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 25, 25, 12, 4, 3, 7, 7, 10, 10, 10, 10, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 49) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CCCS(=O)(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(F)cc1F) `ZINC001631917933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631917933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001631917933 none CCCS(=O)(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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: [29, 27, 14, 12, 14, 14, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 27, 27, 12, 4, 3, 7, 7, 10, 10, 10, 10, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001631917933 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001631917933 Building ZINC001632244936 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632244936 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/50 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)c1ccc(Br)cc1) `ZINC001632244936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632244936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001632244936 none O=C(NCCCNC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 11, 19, 19, 11, 11, 19, 19, 11, 11, 10, 11, 11, 9, 9, 3, 7, 7, 12, 12, 12, 12, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/51 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)c1ccc(Br)cc1) `ZINC001632244936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632244936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001632244936 none O=C(NCCCNC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 10, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 20, 20, 12, 12, 20, 20, 12, 10, 11, 11, 11, 9, 9, 3, 7, 7, 12, 12, 12, 12, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001632244936 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 Building ZINC001632244936 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632244936 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 50) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)c1ccc(Br)cc1) `ZINC001632244936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632244936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001632244936 none O=C(NCCCNC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 11, 19, 19, 11, 11, 19, 19, 11, 11, 10, 11, 11, 9, 9, 3, 7, 7, 12, 12, 12, 12, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 51) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)c1ccc(Br)cc1) `ZINC001632244936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632244936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001632244936 none O=C(NCCCNC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 10, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 20, 20, 12, 12, 20, 20, 12, 10, 11, 11, 11, 9, 9, 3, 7, 7, 12, 12, 12, 12, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001632244936 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632244936 Building ZINC001632374887 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632374887 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/52 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1) `ZINC001632374887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632374887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001632374887 none Cn1cc([C@@H]2C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 3, 14, 14, 14, 14, 14, 14, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 4, 4, 7, 7, 7, 7, 3, 3, 14] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/53 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1) `ZINC001632374887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632374887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001632374887 none Cn1cc([C@@H]2C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 6, 2, 6, 1, 1, 1, 4, 4, 6, 6, 4, 5, 6, 6, 6, 15, 15, 15, 15, 15, 15, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 4, 4, 6, 6, 6, 6, 6, 6, 15] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001632374887 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 Building ZINC001632374887 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632374887 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 52) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cn1cc([C@@H]2C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1) `ZINC001632374887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632374887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001632374887 none Cn1cc([C@@H]2C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 3, 14, 14, 14, 14, 14, 14, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 4, 4, 7, 7, 7, 7, 3, 3, 14] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 53) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cn1cc([C@@H]2C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1) `ZINC001632374887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632374887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001632374887 none Cn1cc([C@@H]2C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 6, 2, 6, 1, 1, 1, 4, 4, 6, 6, 4, 5, 6, 6, 6, 15, 15, 15, 15, 15, 15, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 4, 4, 6, 6, 6, 6, 6, 6, 15] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001632374887 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374887 Building ZINC001632374890 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632374890 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/54 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1) `ZINC001632374890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632374890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001632374890 none Cn1cc([C@@H]2C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 2, 1, 1, 1, 3, 3, 6, 6, 3, 6, 6, 6, 2, 8, 8, 8, 8, 8, 8, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 3, 3, 6, 6, 6, 6, 2, 2, 8] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/55 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1) `ZINC001632374890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632374890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001632374890 none Cn1cc([C@@H]2C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 2, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 2, 11, 11, 11, 11, 11, 11, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 4, 4, 4, 4, 2, 2, 11] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001632374890 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 Building ZINC001632374890 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632374890 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 54) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cn1cc([C@@H]2C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1) `ZINC001632374890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632374890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001632374890 none Cn1cc([C@@H]2C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 2, 1, 1, 1, 3, 3, 6, 6, 3, 6, 6, 6, 2, 8, 8, 8, 8, 8, 8, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 3, 3, 6, 6, 6, 6, 2, 2, 8] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 55) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cn1cc([C@@H]2C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1) `ZINC001632374890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632374890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001632374890 none Cn1cc([C@@H]2C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 2, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 2, 11, 11, 11, 11, 11, 11, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 4, 4, 4, 4, 2, 2, 11] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001632374890 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001632374890 Building ZINC001633104141 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633104141 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/56 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](C#N)c3ccc(Br)cc3)CC2)c1) `ZINC001633104141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633104141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001633104141 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](C#N)c3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 25, 25, 25, 25, 27, 27, 27, 27, 27, 27, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 27, 27, 27, 27, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/57 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](C#N)c3ccc(Br)cc3)CC2)c1) `ZINC001633104141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633104141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001633104141 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](C#N)c3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 23, 23, 23, 23, 26, 26, 26, 26, 26, 26, 12, 12, 6, 6, 6, 6, 2, 6, 6, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633104141 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 Building ZINC001633104141 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633104141 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 56) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](C#N)c3ccc(Br)cc3)CC2)c1) `ZINC001633104141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633104141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001633104141 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](C#N)c3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 25, 25, 25, 25, 27, 27, 27, 27, 27, 27, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 27, 27, 27, 27, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 57) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](C#N)c3ccc(Br)cc3)CC2)c1) `ZINC001633104141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633104141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001633104141 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](C#N)c3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 23, 23, 23, 23, 26, 26, 26, 26, 26, 26, 12, 12, 6, 6, 6, 6, 2, 6, 6, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633104141 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104141 Building ZINC001633104142 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633104142 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/58 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](C#N)c3ccc(Br)cc3)CC2)c1) `ZINC001633104142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633104142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001633104142 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](C#N)c3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 5, 11, 11, 11, 11, 24, 24, 24, 24, 28, 28, 24, 28, 28, 28, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/59 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](C#N)c3ccc(Br)cc3)CC2)c1) `ZINC001633104142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633104142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001633104142 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](C#N)c3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 24, 24, 24, 24, 26, 26, 24, 26, 26, 26, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 26, 26, 26, 26, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633104142 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 Building ZINC001633104142 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633104142 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 58) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](C#N)c3ccc(Br)cc3)CC2)c1) `ZINC001633104142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633104142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001633104142 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](C#N)c3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 5, 11, 11, 11, 11, 24, 24, 24, 24, 28, 28, 24, 28, 28, 28, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 59) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](C#N)c3ccc(Br)cc3)CC2)c1) `ZINC001633104142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633104142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001633104142 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](C#N)c3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 24, 24, 24, 24, 26, 26, 24, 26, 26, 26, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 26, 26, 26, 26, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633104142 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633104142 Building ZINC001633525609 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633525609 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/60 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001633525609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633525609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001633525609 none O=C(N[C@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 1, 1, 1, 9, 9, 11, 11, 9, 9, 11, 11, 3, 12, 12, 17, 17, 17, 17, 17, 17, 12, 12, 9, 9, 11, 11, 11, 11] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/61 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001633525609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633525609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001633525609 none O=C(N[C@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 15, 15, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 15, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 3, 15, 15, 20, 20, 20, 20, 20, 20, 15, 15, 6, 6, 8, 8, 8, 8] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633525609 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 Building ZINC001633525609 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633525609 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 60) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N[C@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001633525609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633525609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001633525609 none O=C(N[C@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 1, 1, 1, 9, 9, 11, 11, 9, 9, 11, 11, 3, 12, 12, 17, 17, 17, 17, 17, 17, 12, 12, 9, 9, 11, 11, 11, 11] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 61) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N[C@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001633525609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633525609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001633525609 none O=C(N[C@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 15, 15, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 15, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 3, 15, 15, 20, 20, 20, 20, 20, 20, 15, 15, 6, 6, 8, 8, 8, 8] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633525609 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525609 Building ZINC001633525612 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633525612 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/62 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001633525612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633525612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001633525612 none O=C(N[C@@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 15, 15, 15, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 15, 1, 1, 1, 7, 7, 9, 9, 7, 7, 9, 9, 3, 15, 15, 19, 19, 19, 19, 19, 19, 15, 15, 7, 7, 9, 9, 9, 9] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/63 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001633525612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633525612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001633525612 none O=C(N[C@@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 1, 1, 1, 9, 9, 11, 11, 11, 11, 11, 11, 3, 12, 12, 17, 17, 17, 17, 17, 17, 12, 12, 9, 9, 11, 11, 11, 11] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633525612 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 Building ZINC001633525612 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633525612 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 62) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N[C@@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001633525612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633525612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001633525612 none O=C(N[C@@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 15, 15, 15, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 15, 1, 1, 1, 7, 7, 9, 9, 7, 7, 9, 9, 3, 15, 15, 19, 19, 19, 19, 19, 19, 15, 15, 7, 7, 9, 9, 9, 9] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 63) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N[C@@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001633525612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633525612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001633525612 none O=C(N[C@@H]1CC(=O)N(Cc2ccccc2C(F)(F)F)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 1, 1, 1, 9, 9, 11, 11, 11, 11, 11, 11, 3, 12, 12, 17, 17, 17, 17, 17, 17, 12, 12, 9, 9, 11, 11, 11, 11] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633525612 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633525612 Building ZINC001633652791 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633652791 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/64 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001633652791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633652791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633652791 none C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 3, 7, 7, 17, 17, 17, 29, 29, 29, 29, 17, 17, 3, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 6, 6, 4, 4, 6, 6, 3, 3, 7, 7, 7, 29, 29, 29, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 85 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/65 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001633652791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633652791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633652791 none C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 6, 12, 12, 23, 23, 23, 37, 37, 37, 37, 23, 23, 6, 6, 6, 4, 1, 2, 1, 1, 1, 4, 4, 6, 6, 4, 4, 6, 6, 6, 6, 12, 12, 12, 37, 37, 37, 6, 6, 6, 6, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633652791 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 Building ZINC001633652791 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633652791 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 64) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001633652791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633652791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633652791 none C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 3, 7, 7, 17, 17, 17, 29, 29, 29, 29, 17, 17, 3, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 6, 6, 4, 4, 6, 6, 3, 3, 7, 7, 7, 29, 29, 29, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 85 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 65) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001633652791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633652791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633652791 none C[C@@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 6, 12, 12, 23, 23, 23, 37, 37, 37, 37, 23, 23, 6, 6, 6, 4, 1, 2, 1, 1, 1, 4, 4, 6, 6, 4, 4, 6, 6, 6, 6, 12, 12, 12, 37, 37, 37, 6, 6, 6, 6, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633652791 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652791 Building ZINC001633652793 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633652793 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/66 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001633652793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633652793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633652793 none C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 7, 18, 18, 18, 30, 30, 30, 30, 18, 18, 4, 4, 4, 3, 1, 2, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 4, 4, 7, 7, 7, 30, 30, 30, 4, 4, 4, 4, 3, 3, 5, 5, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 78 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/67 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001633652793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633652793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633652793 none C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 7, 12, 12, 25, 25, 25, 36, 36, 36, 36, 25, 25, 7, 7, 7, 4, 1, 2, 1, 1, 1, 3, 3, 6, 6, 3, 3, 6, 6, 7, 7, 12, 12, 12, 36, 36, 36, 7, 7, 7, 7, 3, 3, 6, 6, 6, 6, 7, 7, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633652793 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 Building ZINC001633652793 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633652793 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 66) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001633652793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633652793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633652793 none C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 7, 18, 18, 18, 30, 30, 30, 30, 18, 18, 4, 4, 4, 3, 1, 2, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 4, 4, 7, 7, 7, 30, 30, 30, 4, 4, 4, 4, 3, 3, 5, 5, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 78 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 67) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1) `ZINC001633652793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633652793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633652793 none C[C@H](c1nc(c2cccs2)no1)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 7, 12, 12, 25, 25, 25, 36, 36, 36, 36, 25, 25, 7, 7, 7, 4, 1, 2, 1, 1, 1, 3, 3, 6, 6, 3, 3, 6, 6, 7, 7, 12, 12, 12, 36, 36, 36, 7, 7, 7, 7, 3, 3, 6, 6, 6, 6, 7, 7, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633652793 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633652793 Building ZINC001633753031 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633753031 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/68 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)c(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1) `ZINC001633753031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633753031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633753031 none COc1cc(OC)c(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 16, 16, 16, 16, 16, 19, 15, 10, 10, 10, 10, 10, 7, 3, 1, 3, 1, 1, 1, 5, 5, 9, 9, 5, 5, 9, 9, 16, 16, 19, 16, 25, 26, 26, 16, 19, 19, 19, 15, 15, 10, 10, 7, 5, 5, 9, 9, 9, 9, 19, 19, 19, 16] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/69 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)c(Cn2nccc2NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1) `ZINC001633753031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633753031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633753031 none COc1cc(OC)c(Cn2nccc2NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 18, 21, 16, 10, 10, 10, 10, 10, 7, 3, 1, 3, 1, 1, 1, 6, 6, 9, 9, 6, 6, 9, 9, 18, 18, 21, 18, 28, 28, 28, 18, 21, 21, 21, 16, 16, 10, 10, 7, 6, 6, 9, 9, 9, 9, 21, 21, 21, 18] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633753031 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 Building ZINC001633753031 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633753031 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 68) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COc1cc(OC)c(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1) `ZINC001633753031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633753031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633753031 none COc1cc(OC)c(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 16, 16, 16, 16, 16, 19, 15, 10, 10, 10, 10, 10, 7, 3, 1, 3, 1, 1, 1, 5, 5, 9, 9, 5, 5, 9, 9, 16, 16, 19, 16, 25, 26, 26, 16, 19, 19, 19, 15, 15, 10, 10, 7, 5, 5, 9, 9, 9, 9, 19, 19, 19, 16] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 69) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COc1cc(OC)c(Cn2nccc2NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1) `ZINC001633753031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633753031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633753031 none COc1cc(OC)c(Cn2nccc2NC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 18, 21, 16, 10, 10, 10, 10, 10, 7, 3, 1, 3, 1, 1, 1, 6, 6, 9, 9, 6, 6, 9, 9, 18, 18, 21, 18, 28, 28, 28, 18, 21, 21, 21, 16, 16, 10, 10, 7, 6, 6, 9, 9, 9, 9, 21, 21, 21, 18] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001633753031 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001633753031 Building ZINC001634165031 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634165031 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/70 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1cccnc1)C1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1)C(F)(F)F) `ZINC001634165031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634165031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001634165031 none O=C(N(c1cccnc1)C1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 23, 23, 23, 23, 23, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 9, 9, 6, 6, 9, 9, 3, 3, 13, 13, 13, 13, 23, 23, 23, 23, 3, 3, 3, 3, 3, 6, 6, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/71 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1cccnc1)C1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1)C(F)(F)F) `ZINC001634165031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634165031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001634165031 none O=C(N(c1cccnc1)C1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 14, 21, 21, 21, 21, 21, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 5, 5, 14, 14, 14, 14, 21, 21, 21, 21, 5, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634165031 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 Building ZINC001634165031 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634165031 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 70) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1cccnc1)C1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1)C(F)(F)F) `ZINC001634165031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634165031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001634165031 none O=C(N(c1cccnc1)C1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 23, 23, 23, 23, 23, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 9, 9, 6, 6, 9, 9, 3, 3, 13, 13, 13, 13, 23, 23, 23, 23, 3, 3, 3, 3, 3, 6, 6, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 71) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1cccnc1)C1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1)C(F)(F)F) `ZINC001634165031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634165031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001634165031 none O=C(N(c1cccnc1)C1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 14, 21, 21, 21, 21, 21, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 5, 5, 14, 14, 14, 14, 21, 21, 21, 21, 5, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634165031 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634165031 Building ZINC001634249072 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634249072 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/72 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Cc2nc(c3ccc(F)cn3)no2)CC1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634249072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634249072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001634249072 none O=C(N1CCC(Cc2nc(c3ccc(F)cn3)no2)CC1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 8, 8, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 9, 34, 34, 34, 38, 38, 38, 38, 38, 38, 34, 34, 3, 3, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 3, 3, 3, 3, 3, 9, 9, 38, 38, 38, 3, 3, 3, 3, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/73 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Cc2nc(c3ccc(F)cn3)no2)CC1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634249072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634249072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001634249072 none O=C(N1CCC(Cc2nc(c3ccc(F)cn3)no2)CC1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 8, 8, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 2, 7, 28, 28, 28, 35, 35, 35, 35, 35, 35, 28, 28, 2, 2, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 2, 2, 2, 2, 2, 7, 7, 35, 35, 35, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634249072 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 Building ZINC001634249072 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634249072 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 72) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N1CCC(Cc2nc(c3ccc(F)cn3)no2)CC1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634249072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634249072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001634249072 none O=C(N1CCC(Cc2nc(c3ccc(F)cn3)no2)CC1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 8, 8, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 9, 34, 34, 34, 38, 38, 38, 38, 38, 38, 34, 34, 3, 3, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 3, 3, 3, 3, 3, 9, 9, 38, 38, 38, 3, 3, 3, 3, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 73) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N1CCC(Cc2nc(c3ccc(F)cn3)no2)CC1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634249072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634249072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001634249072 none O=C(N1CCC(Cc2nc(c3ccc(F)cn3)no2)CC1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 8, 8, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 2, 7, 28, 28, 28, 35, 35, 35, 35, 35, 35, 28, 28, 2, 2, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 2, 2, 2, 2, 2, 7, 7, 35, 35, 35, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634249072 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634249072 Building ZINC001634293325 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634293325 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/74 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1)[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634293325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634293325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 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: ZINC001634293325 none O=C(NCc1ccccc1)[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 21, 25, 25, 21, 25, 25, 2, 3, 3, 7, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 7, 7, 11, 11, 7, 11, 11, 11, 7, 21, 21, 25, 25, 21, 25, 25, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/75 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1)[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634293325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634293325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 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: ZINC001634293325 none O=C(NCc1ccccc1)[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 25, 28, 28, 25, 28, 28, 3, 5, 5, 8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 8, 25, 25, 28, 28, 25, 28, 28, 8, 8, 8, 8, 8, 8, 8, 3, 7, 7, 10, 10, 10, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634293325 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 Building ZINC001634293325 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634293325 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 74) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(NCc1ccccc1)[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634293325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634293325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 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: ZINC001634293325 none O=C(NCc1ccccc1)[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 21, 25, 25, 21, 25, 25, 2, 3, 3, 7, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 7, 7, 11, 11, 7, 11, 11, 11, 7, 21, 21, 25, 25, 21, 25, 25, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 75) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(NCc1ccccc1)[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634293325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634293325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 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: ZINC001634293325 none O=C(NCc1ccccc1)[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 25, 28, 28, 25, 28, 28, 3, 5, 5, 8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 8, 25, 25, 28, 28, 25, 28, 28, 8, 8, 8, 8, 8, 8, 8, 3, 7, 7, 10, 10, 10, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634293325 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293325 Building ZINC001634293326 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634293326 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/76 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634293326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634293326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 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: ZINC001634293326 none O=C(NCc1ccccc1)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 25, 28, 28, 27, 28, 28, 3, 5, 5, 8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 7, 7, 10, 10, 8, 25, 25, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 8, 3, 7, 7, 10, 10, 10, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/77 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634293326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634293326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 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: ZINC001634293326 none O=C(NCc1ccccc1)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 20, 23, 23, 23, 23, 23, 2, 3, 3, 7, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 7, 7, 11, 11, 7, 7, 11, 11, 6, 20, 20, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634293326 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 Building ZINC001634293326 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634293326 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 76) grep: /scratch/xiaobo/372095/xaa-8058088.1/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(NCc1ccccc1)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634293326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634293326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 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: ZINC001634293326 none O=C(NCc1ccccc1)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 25, 28, 28, 27, 28, 28, 3, 5, 5, 8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 7, 7, 10, 10, 7, 7, 10, 10, 8, 25, 25, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 8, 3, 7, 7, 10, 10, 10, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 77) grep: /scratch/xiaobo/372095/xaa-8058088.1/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(NCc1ccccc1)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001634293326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634293326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 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: ZINC001634293326 none O=C(NCc1ccccc1)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 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: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 20, 23, 23, 23, 23, 23, 2, 3, 3, 7, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 7, 7, 11, 11, 7, 7, 11, 11, 6, 20, 20, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 7, 7, 2, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634293326 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634293326 Building ZINC001634572837 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634572837 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/78 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)ccc1[N+](=O)[O-]) `ZINC001634572837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634572837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001634572837 none CCOc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)ccc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 19, 19, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 35, 35, 35, 35, 35, 19, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/79 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)ccc1[N+](=O)[O-]) `ZINC001634572837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634572837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001634572837 none CCOc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)ccc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 18, 18, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 4, 4, 18, 18, 18, 18, 18, 18, 35, 35, 35, 35, 35, 18, 4, 4, 4, 4, 3, 3, 5, 5, 5, 5, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634572837 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 Building ZINC001634572837 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634572837 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 78) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CCOc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)ccc1[N+](=O)[O-]) `ZINC001634572837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634572837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001634572837 none CCOc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)ccc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 19, 19, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 35, 35, 35, 35, 35, 19, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 79) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: CCOc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)ccc1[N+](=O)[O-]) `ZINC001634572837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634572837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001634572837 none CCOc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)ccc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 18, 18, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 4, 4, 18, 18, 18, 18, 18, 18, 35, 35, 35, 35, 35, 18, 4, 4, 4, 4, 3, 3, 5, 5, 5, 5, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634572837 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634572837 Building ZINC001634938913 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634938913 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/80 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)C2(NC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CCCC2)cc1OC) `ZINC001634938913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634938913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001634938913 none COc1ccc(NC(=O)C2(NC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CCCC2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 12, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 5, 5, 9, 9, 5, 5, 9, 9, 3, 3, 3, 3, 12, 12, 12, 21, 22, 22, 22, 12, 12, 3, 2, 5, 5, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 12, 21, 21, 21] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/81 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)C2(NC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CCCC2)cc1OC) `ZINC001634938913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634938913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001634938913 none COc1ccc(NC(=O)C2(NC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CCCC2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 3, 3, 3, 3, 12, 12, 12, 23, 24, 24, 24, 12, 12, 3, 3, 5, 5, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 12, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634938913 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 Building ZINC001634938913 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634938913 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 80) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COc1ccc(NC(=O)C2(NC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CCCC2)cc1OC) `ZINC001634938913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634938913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001634938913 none COc1ccc(NC(=O)C2(NC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CCCC2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 12, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 5, 5, 9, 9, 5, 5, 9, 9, 3, 3, 3, 3, 12, 12, 12, 21, 22, 22, 22, 12, 12, 3, 2, 5, 5, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 12, 21, 21, 21] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 81) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COc1ccc(NC(=O)C2(NC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CCCC2)cc1OC) `ZINC001634938913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634938913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001634938913 none COc1ccc(NC(=O)C2(NC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CCCC2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 1, 1, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 3, 3, 3, 3, 12, 12, 12, 23, 24, 24, 24, 12, 12, 3, 3, 5, 5, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 12, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001634938913 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001634938913 Building ZINC001635417165 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635417165 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/82 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2cccc(Br)c2)C1=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635417165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635417165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635417165 none O=C(N[C@H]1CCN(c2cccc(Br)c2)C1=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 9, 9, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 3, 9, 9, 9, 9, 18, 18, 18, 18, 7, 7, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/83 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2cccc(Br)c2)C1=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635417165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635417165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635417165 none O=C(N[C@H]1CCN(c2cccc(Br)c2)C1=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 9, 9, 1, 1, 1, 7, 7, 10, 10, 7, 7, 10, 10, 3, 9, 9, 9, 9, 18, 18, 18, 18, 7, 7, 10, 10, 10, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001635417165 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 Building ZINC001635417165 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635417165 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 82) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N[C@H]1CCN(c2cccc(Br)c2)C1=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635417165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635417165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635417165 none O=C(N[C@H]1CCN(c2cccc(Br)c2)C1=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 9, 9, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 3, 9, 9, 9, 9, 18, 18, 18, 18, 7, 7, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 83) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N[C@H]1CCN(c2cccc(Br)c2)C1=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635417165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635417165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635417165 none O=C(N[C@H]1CCN(c2cccc(Br)c2)C1=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 9, 9, 1, 1, 1, 7, 7, 10, 10, 7, 7, 10, 10, 3, 9, 9, 9, 9, 18, 18, 18, 18, 7, 7, 10, 10, 10, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001635417165 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417165 Building ZINC001635417166 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635417166 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/84 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2cccc(Br)c2)C1=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635417166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635417166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635417166 none O=C(N[C@@H]1CCN(c2cccc(Br)c2)C1=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 7, 7, 10, 10, 7, 10, 10, 10, 3, 8, 8, 8, 8, 16, 16, 16, 16, 7, 7, 10, 10, 10, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/85 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2cccc(Br)c2)C1=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635417166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635417166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635417166 none O=C(N[C@@H]1CCN(c2cccc(Br)c2)C1=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 9, 9, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 3, 9, 9, 9, 9, 18, 18, 18, 18, 6, 6, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001635417166 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 Building ZINC001635417166 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635417166 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 84) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N[C@@H]1CCN(c2cccc(Br)c2)C1=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635417166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635417166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635417166 none O=C(N[C@@H]1CCN(c2cccc(Br)c2)C1=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 7, 7, 10, 10, 7, 10, 10, 10, 3, 8, 8, 8, 8, 16, 16, 16, 16, 7, 7, 10, 10, 10, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 85) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(N[C@@H]1CCN(c2cccc(Br)c2)C1=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635417166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635417166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635417166 none O=C(N[C@@H]1CCN(c2cccc(Br)c2)C1=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 9, 9, 1, 1, 1, 6, 6, 7, 7, 6, 6, 7, 7, 3, 9, 9, 9, 9, 18, 18, 18, 18, 6, 6, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001635417166 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635417166 Building ZINC001635771980 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635771980 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/86 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Br)cc1N1CCOCC1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635771980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635771980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635771980 none O=C(NCc1ccc(Br)cc1N1CCOCC1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 3, 12, 12, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 10, 10, 10, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/87 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Br)cc1N1CCOCC1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635771980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635771980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635771980 none O=C(NCc1ccc(Br)cc1N1CCOCC1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 3, 12, 12, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001635771980 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 Building ZINC001635771980 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635771980 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 86) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(NCc1ccc(Br)cc1N1CCOCC1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635771980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635771980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635771980 none O=C(NCc1ccc(Br)cc1N1CCOCC1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 3, 12, 12, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 10, 10, 10, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 87) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: O=C(NCc1ccc(Br)cc1N1CCOCC1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001635771980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635771980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635771980 none O=C(NCc1ccc(Br)cc1N1CCOCC1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 3, 12, 12, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001635771980 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001635771980 Building ZINC001636173082 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636173082 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/88 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 20, 14, 20, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 4, 4, 7, 7, 4, 4, 7, 7, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/89 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 20, 14, 20, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 4, 4, 7, 7, 4, 4, 7, 7, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/90 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/90' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 27, 27, 22, 13, 22, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `3' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 3 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/91 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/91' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 27, 27, 22, 13, 22, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001636173082 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2.* 3: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 Building ZINC001636173082 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636173082 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 88) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 20, 14, 20, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 4, 4, 7, 7, 4, 4, 7, 7, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 89) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 20, 14, 20, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 4, 4, 7, 7, 4, 4, 7, 7, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 90) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 27, 27, 22, 13, 22, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `3' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 3 (index: 91) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 27, 27, 22, 13, 22, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001636173082 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2.* 3: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 Building ZINC001636173082 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636173082 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 88) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 20, 14, 20, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 4, 4, 7, 7, 4, 4, 7, 7, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 89) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 20, 14, 20, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 4, 4, 7, 7, 4, 4, 7, 7, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 90) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 27, 27, 22, 13, 22, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `3' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 3 (index: 91) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 27, 27, 22, 13, 22, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001636173082 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2.* 3: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 Building ZINC001636173082 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636173082 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 88) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 20, 14, 20, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 4, 4, 7, 7, 4, 4, 7, 7, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 89) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 20, 14, 20, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 4, 4, 7, 7, 4, 4, 7, 7, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 90) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 27, 27, 22, 13, 22, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `3' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 3 (index: 91) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2) `ZINC001636173082.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636173082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001636173082 none CC(C)(C)OC(=O)NC1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 27, 27, 22, 13, 22, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001636173082 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/2.* 3: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/3.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636173082 Building ZINC001636713658 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636713658 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/92 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1ccc(F)c(Br)c1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001636713658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636713658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001636713658 none O=C(NC[C@@H](CO)Cc1ccc(F)c(Br)c1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 9, 9, 11, 9, 14, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 6, 6, 5, 6, 6, 6, 2, 5, 5, 11, 11, 33, 14, 14, 23, 23, 23, 3, 3, 6, 6, 6, 6] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/93 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001636713658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636713658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001636713658 none O=C(NC[C@@H](CO)Cc1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 6, 10, 10, 10, 10, 14, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 2, 6, 6, 10, 10, 30, 14, 14, 24, 24, 24, 5, 5, 8, 8, 8, 8] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001636713658 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 Building ZINC001636713658 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636713658 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 92) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1ccc(F)c(Br)c1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001636713658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636713658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001636713658 none O=C(NC[C@@H](CO)Cc1ccc(F)c(Br)c1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 9, 9, 11, 9, 14, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 6, 6, 5, 6, 6, 6, 2, 5, 5, 11, 11, 33, 14, 14, 23, 23, 23, 3, 3, 6, 6, 6, 6] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 93) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001636713658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636713658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001636713658 none O=C(NC[C@@H](CO)Cc1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 6, 10, 10, 10, 10, 14, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 2, 6, 6, 10, 10, 30, 14, 14, 24, 24, 24, 5, 5, 8, 8, 8, 8] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001636713658 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713658 Building ZINC001636713659 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636713659 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/94 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1ccc(F)c(Br)c1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001636713659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636713659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001636713659 none O=C(NC[C@H](CO)Cc1ccc(F)c(Br)c1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 6, 10, 10, 10, 10, 14, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 2, 6, 6, 10, 10, 30, 14, 14, 25, 25, 25, 5, 5, 7, 7, 7, 7] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/95 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001636713659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636713659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001636713659 none O=C(NC[C@H](CO)Cc1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 9, 9, 11, 9, 14, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 6, 6, 3, 3, 6, 6, 2, 5, 5, 11, 11, 33, 14, 14, 23, 23, 23, 3, 3, 6, 6, 6, 6] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 149 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001636713659 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 Building ZINC001636713659 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636713659 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 94) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1ccc(F)c(Br)c1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001636713659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636713659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001636713659 none O=C(NC[C@H](CO)Cc1ccc(F)c(Br)c1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 6, 10, 10, 10, 10, 14, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 2, 6, 6, 10, 10, 30, 14, 14, 25, 25, 25, 5, 5, 7, 7, 7, 7] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 95) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001636713659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636713659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001636713659 none O=C(NC[C@H](CO)Cc1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 9, 9, 11, 9, 14, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 6, 6, 3, 3, 6, 6, 2, 5, 5, 11, 11, 33, 14, 14, 23, 23, 23, 3, 3, 6, 6, 6, 6] 150 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 149 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001636713659 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001636713659 Building ZINC001638268275 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638268275 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/96 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cn2cc(CCNC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)nc12) `ZINC001638268275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638268275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001638268275 none Cc1cc(Br)cn2cc(CCNC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 21, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 21, 21, 12, 12, 3, 6, 6, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/97 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cn2cc(CCNC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)nc12) `ZINC001638268275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638268275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001638268275 none Cc1cc(Br)cn2cc(CCNC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 21, 13, 3, 3, 1, 3, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 13, 13, 3, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001638268275 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 Building ZINC001638268275 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638268275 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 96) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1cc(Br)cn2cc(CCNC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)nc12) `ZINC001638268275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638268275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001638268275 none Cc1cc(Br)cn2cc(CCNC(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 21, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 21, 21, 12, 12, 3, 6, 6, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 97) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: Cc1cc(Br)cn2cc(CCNC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)nc12) `ZINC001638268275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638268275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001638268275 none Cc1cc(Br)cn2cc(CCNC(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 21, 13, 3, 3, 1, 3, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 13, 13, 3, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001638268275 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001638268275 Building ZINC001639462786 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639462786 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/98 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 13, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 3, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 10, 10, 10, 10] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/99 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 14, 26, 26, 26, 26, 26, 25, 1, 1, 1, 9, 9, 12, 12, 10, 12, 12, 12, 3, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/100 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/100' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 13, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 3, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 10, 10, 10, 10] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `3' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 3 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/101 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/101' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 14, 26, 26, 26, 26, 26, 25, 1, 1, 1, 9, 9, 12, 12, 10, 12, 12, 12, 3, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639462786 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2.* 3: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 Building ZINC001639462786 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639462786 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 98) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 13, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 3, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 10, 10, 10, 10] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 99) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 14, 26, 26, 26, 26, 26, 25, 1, 1, 1, 9, 9, 12, 12, 10, 12, 12, 12, 3, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 100) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 13, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 3, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 10, 10, 10, 10] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `3' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 3 (index: 101) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 14, 26, 26, 26, 26, 26, 25, 1, 1, 1, 9, 9, 12, 12, 10, 12, 12, 12, 3, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639462786 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2.* 3: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 Building ZINC001639462786 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639462786 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 98) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 13, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 3, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 10, 10, 10, 10] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 99) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 14, 26, 26, 26, 26, 26, 25, 1, 1, 1, 9, 9, 12, 12, 10, 12, 12, 12, 3, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 100) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 13, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 3, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 10, 10, 10, 10] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `3' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 3 (index: 101) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 14, 26, 26, 26, 26, 26, 25, 1, 1, 1, 9, 9, 12, 12, 10, 12, 12, 12, 3, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639462786 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2.* 3: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 Building ZINC001639462786 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639462786 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 98) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 13, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 3, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 10, 10, 10, 10] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 99) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 14, 26, 26, 26, 26, 26, 25, 1, 1, 1, 9, 9, 12, 12, 10, 12, 12, 12, 3, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `2' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 2 (index: 100) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 13, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 10, 3, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 10, 10, 10, 10] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `3' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 3 (index: 101) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639462786.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639462786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001639462786 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCNC(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 6, 8, 8, 14, 26, 26, 26, 26, 26, 25, 1, 1, 1, 9, 9, 12, 12, 10, 12, 12, 12, 3, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639462786 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/1.* 2: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/2.* 3: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/3.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639462786 Building ZINC001639778121 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639778121 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/102 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(OC2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)C1) `ZINC001639778121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639778121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001639778121 none CC(C)(C)OC(=O)N1CC(OC2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 15, 26, 15, 15, 8, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 3, 3, 3, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/103 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(OC2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)C1) `ZINC001639778121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639778121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001639778121 none CC(C)(C)OC(=O)N1CC(OC2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 41, 23, 23, 9, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 3, 3, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 23, 23, 23, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 4, 3, 3, 3, 3, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639778121 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 Building ZINC001639778121 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639778121 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 102) grep: /scratch/xiaobo/372095/xaa-8058088.1/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)OC(=O)N1CC(OC2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)C1) `ZINC001639778121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639778121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001639778121 none CC(C)(C)OC(=O)N1CC(OC2CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 15, 26, 15, 15, 8, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 3, 3, 3, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 103) grep: /scratch/xiaobo/372095/xaa-8058088.1/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)OC(=O)N1CC(OC2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)C1) `ZINC001639778121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639778121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001639778121 none CC(C)(C)OC(=O)N1CC(OC2CCN(C(=O)[C@]([O-])([SiH3])/C=C/c3ccc(F)cc3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 41, 23, 23, 9, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 4, 4, 2, 2, 4, 4, 3, 3, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 23, 23, 23, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 4, 3, 3, 3, 3, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639778121 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639778121 Building ZINC001639983103 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639983103 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/104 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639983103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639983103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639983103 none COC(=O)[C@@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 7, 15, 3, 7, 7, 12, 12, 12, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 6, 6, 10, 10, 6, 6, 10, 10, 15, 15, 15, 12, 12, 12, 12, 12, 12, 3, 6, 6, 10, 10, 10, 10] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/105 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639983103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639983103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639983103 none COC(=O)[C@@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 6, 15, 2, 6, 6, 10, 11, 11, 10, 11, 11, 11, 2, 1, 2, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 15, 15, 15, 10, 10, 11, 11, 11, 11, 2, 6, 6, 11, 11, 11, 11] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639983103 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 Building ZINC001639983103 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639983103 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 104) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COC(=O)[C@@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639983103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639983103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639983103 none COC(=O)[C@@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 7, 15, 3, 7, 7, 12, 12, 12, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 6, 6, 10, 10, 6, 6, 10, 10, 15, 15, 15, 12, 12, 12, 12, 12, 12, 3, 6, 6, 10, 10, 10, 10] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 105) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COC(=O)[C@@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639983103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639983103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639983103 none COC(=O)[C@@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 6, 15, 2, 6, 6, 10, 11, 11, 10, 11, 11, 11, 2, 1, 2, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 15, 15, 15, 10, 10, 11, 11, 11, 11, 2, 6, 6, 11, 11, 11, 11] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639983103 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983103 Building ZINC001639983204 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639983204 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/106 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639983204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639983204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639983204 none COC(=O)[C@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 6, 15, 2, 6, 6, 10, 11, 11, 10, 11, 11, 11, 2, 1, 2, 1, 1, 1, 6, 6, 11, 11, 6, 6, 11, 11, 15, 15, 15, 10, 10, 11, 11, 11, 11, 2, 6, 6, 11, 11, 11, 11] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/107 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639983204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639983204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639983204 none COC(=O)[C@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 16, 3, 7, 7, 12, 12, 12, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 16, 16, 16, 12, 12, 12, 12, 12, 12, 3, 6, 6, 10, 10, 10, 10] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639983204 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 Building ZINC001639983204 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639983204 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 106) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COC(=O)[C@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639983204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639983204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639983204 none COC(=O)[C@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 6, 15, 2, 6, 6, 10, 11, 11, 10, 11, 11, 11, 2, 1, 2, 1, 1, 1, 6, 6, 11, 11, 6, 6, 11, 11, 15, 15, 15, 10, 10, 11, 11, 11, 11, 2, 6, 6, 11, 11, 11, 11] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 107) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: COC(=O)[C@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001639983204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639983204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639983204 none COC(=O)[C@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 16, 3, 7, 7, 12, 12, 12, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 16, 16, 16, 12, 12, 12, 12, 12, 12, 3, 6, 6, 10, 10, 10, 10] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639983204 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639983204 Building ZINC001639989142 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639989142 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/108 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#Cc1ccc(c2cc(N3CCN(C(=O)[C@]([O-])([SiH3])/C=C/c4ccc(F)cc4)CC3)n[nH]2)cc1) `ZINC001639989142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639989142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001639989142 none N#Cc1ccc(c2cc(N3CCN(C(=O)[C@]([O-])([SiH3])/C=C/c4ccc(F)cc4)CC3)n[nH]2)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 36, 36, 14, 14, 14, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 3, 3, 6, 6, 3, 3, 6, 6, 4, 4, 14, 14, 14, 36, 36, 36, 36, 14, 4, 4, 4, 4, 3, 3, 6, 6, 6, 6, 4, 4, 4, 4, 36, 36] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/109 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#Cc1ccc(c2cc(N3CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c4ccc(F)cc4)CC3)n[nH]2)cc1) `ZINC001639989142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639989142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001639989142 none N#Cc1ccc(c2cc(N3CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c4ccc(F)cc4)CC3)n[nH]2)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 34, 34, 16, 16, 16, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 3, 3, 6, 6, 3, 3, 6, 6, 5, 5, 16, 16, 16, 34, 34, 34, 34, 16, 5, 5, 5, 5, 3, 3, 6, 6, 6, 6, 5, 5, 5, 5, 34, 34] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639989142 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 Building ZINC001639989142 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639989142 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 108) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: N#Cc1ccc(c2cc(N3CCN(C(=O)[C@]([O-])([SiH3])/C=C/c4ccc(F)cc4)CC3)n[nH]2)cc1) `ZINC001639989142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639989142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001639989142 none N#Cc1ccc(c2cc(N3CCN(C(=O)[C@]([O-])([SiH3])/C=C/c4ccc(F)cc4)CC3)n[nH]2)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 36, 36, 14, 14, 14, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 3, 3, 6, 6, 3, 3, 6, 6, 4, 4, 14, 14, 14, 36, 36, 36, 36, 14, 4, 4, 4, 4, 3, 3, 6, 6, 6, 6, 4, 4, 4, 4, 36, 36] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 109) grep: /scratch/xiaobo/372095/xaa-8058088.1/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: N#Cc1ccc(c2cc(N3CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c4ccc(F)cc4)CC3)n[nH]2)cc1) `ZINC001639989142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639989142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001639989142 none N#Cc1ccc(c2cc(N3CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c4ccc(F)cc4)CC3)n[nH]2)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 34, 34, 16, 16, 16, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 3, 3, 6, 6, 3, 3, 6, 6, 5, 5, 16, 16, 16, 34, 34, 34, 34, 16, 5, 5, 5, 5, 3, 3, 6, 6, 6, 6, 5, 5, 5, 5, 34, 34] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001639989142 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001639989142 Building ZINC001643341616 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643341616 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/110 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc(Br)cc2)C(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001643341616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643341616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001643341616 none O=C(N1CCN(Cc2ccc(Br)cc2)C(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 7, 8, 8, 8, 8, 22, 26, 26, 23, 26, 26, 26, 8, 8, 8, 1, 1, 1, 4, 4, 7, 7, 4, 4, 7, 7, 8, 8, 8, 8, 22, 22, 26, 26, 26, 26, 8, 8, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/111 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc(Br)cc2)C(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001643341616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643341616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001643341616 none O=C(N1CCN(Cc2ccc(Br)cc2)C(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 8, 8, 8, 8, 20, 25, 25, 23, 25, 25, 25, 8, 8, 8, 1, 1, 1, 4, 4, 7, 7, 6, 7, 7, 7, 8, 8, 8, 8, 20, 20, 25, 25, 25, 25, 8, 8, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001643341616 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 Building ZINC001643341616 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643341616 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 110) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc(Br)cc2)C(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001643341616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643341616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001643341616 none O=C(N1CCN(Cc2ccc(Br)cc2)C(=O)C1)[C@@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 7, 8, 8, 8, 8, 22, 26, 26, 23, 26, 26, 26, 8, 8, 8, 1, 1, 1, 4, 4, 7, 7, 4, 4, 7, 7, 8, 8, 8, 8, 22, 22, 26, 26, 26, 26, 8, 8, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 mkdir: created directory `1' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/1 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 1 (index: 111) grep: /scratch/xiaobo/372095/xaa-8058088.1/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc(Br)cc2)C(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1) `ZINC001643341616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643341616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001643341616 none O=C(N1CCN(Cc2ccc(Br)cc2)C(=O)C1)[C@]([O-])([SiH3])/C=C/c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 8, 8, 8, 8, 20, 25, 25, 23, 25, 25, 25, 8, 8, 8, 1, 1, 1, 4, 4, 7, 7, 6, 7, 7, 7, 8, 8, 8, 8, 20, 20, 25, 25, 25, 25, 8, 8, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Finished preparing ZINC001643341616 Recording results /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Appending to /scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.* 1: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/1.* 0: /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616/0.* Removing working files in /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643341616 Building ZINC001643838682 mkdir: created directory `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643838682 mkdir: created directory `0' /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0 /scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682 /scratch/xiaobo/372095/xaa-8058088.1/working /scratch/xiaobo/372095/xaa-8058088.1 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/372095/xaa-8058088.1/working/3D/112 `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/112' -> `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)Nc1ccc2cc(B3OC(C)(C)C(C)(C)O3)ccc2c1) `ZINC001643838682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643838682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. ============================== *** Open Babel Warning in ReadMolecule This Mol2 file is non-standard. Problem with molecule: ZINC001643838682 Cannot interpret atom types correctly, instead attempting to interpret atom type: Du as elements instead. ============================== *** Open Babel Warning in GetAtomicNum Cannot understand the element label Du. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) 1 C -0.10 -3.08 8.04 71.23 0.57 -2.50 16 2 C 0.05 1.96 6.99 43.10 0.30 2.26 16 3 N -0.31 -11.21 12.58 -47.39 -0.60 -11.80 16 4 N -0.38 -13.19 4.01 -356.02 -1.43 -14.61 16 5 C 0.10 2.11 11.09 127.77 1.42 3.52 16 6 C 0.09 3.62 6.86 41.41 0.28 3.91 16 7 C -0.06 -2.46 9.07 71.24 0.65 -1.82 16 8 C -0.24 -10.95 4.27 -20.14 -0.09 -11.04 16 9 C 0.03 1.35 0.44 29.10 0.01 1.37 16 10 O -0.89 -61.40 16.37 -130.06 -2.13 -63.53 16 11 Si 0.94 42.35 21.71 68.60 1.49 43.84 16 12 H -0.18 -5.31 4.66 99.48 0.46 -4.85 16 13 H -0.29 -13.77 6.63 99.48 0.66 -13.11 16 14 H -0.33 -16.51 7.11 99.48 0.71 -15.81 16 15 C 0.49 23.94 4.83 87.66 0.42 24.37 16 16 O -0.56 -31.37 13.56 15.90 0.22 -31.16 16 17 N -0.67 -23.75 4.89 -303.58 -1.49 -25.24 16 18 C 0.17 5.08 6.34 38.24 0.24 5.33 16 19 C -0.13 -4.16 8.62 22.16 0.19 -3.97 16 20 C -0.08 -1.96 9.74 22.33 0.22 -1.75 16 21 C -0.05 -1.04 5.74 -21.28 -0.12 -1.16 16 22 C -0.09 -2.01 9.77 22.79 0.22 -1.79 16 23 C 0.23 5.49 10.45 22.86 0.24 5.73 16 24 O -0.58 -21.02 14.15 -125.77 -1.78 -22.80 16 25 C 0.14 3.60 1.56 -10.38 -0.02 3.58 16 26 C -0.14 -2.93 7.78 71.98 0.56 -2.37 16 27 C -0.15 -2.89 7.77 71.98 0.56 -2.33 16 28 C 0.14 3.41 1.57 -10.38 -0.02 3.40 16 29 C -0.14 -2.76 7.78 71.98 0.56 -2.20 16 30 C -0.15 -2.66 7.79 71.98 0.56 -2.10 16 31 O -0.57 -19.71 14.19 -125.77 -1.79 -21.49 16 32 C -0.11 -1.92 9.92 22.23 0.22 -1.70 16 33 C -0.04 -0.49 9.73 22.31 0.22 -0.27 16 34 C -0.04 -0.68 5.74 -21.26 -0.12 -0.81 16 35 C -0.14 -2.91 9.68 22.67 0.22 -2.69 16 36 H 0.12 2.68 6.58 -2.39 -0.02 2.66 16 37 H 0.10 2.43 8.14 -2.38 -0.02 2.41 16 38 H 0.06 1.99 3.29 -2.38 -0.01 1.98 16 39 H 0.09 1.57 8.14 -2.38 -0.02 1.55 16 40 H 0.09 1.82 7.67 -2.39 -0.02 1.81 16 41 H 0.10 1.85 8.14 -2.38 -0.02 1.83 16 42 H 0.06 2.64 8.14 -2.39 -0.02 2.62 16 43 H 0.09 2.72 7.74 -2.39 -0.02 2.70 16 44 H 0.05 2.49 6.79 -2.38 -0.02 2.47 16 45 H 0.42 12.21 8.04 -92.71 -0.75 11.47 16 46 H 0.12 4.99 5.90 -2.91 -0.02 4.97 16 47 H 0.15 3.30 8.06 -2.91 -0.02 3.28 16 48 H 0.17 3.73 8.06 -2.91 -0.02 3.71 16 49 H 0.09 1.25 6.90 -2.39 -0.02 1.23 16 50 H 0.07 1.36 8.14 -2.39 -0.02 1.34 16 51 H 0.05 1.21 6.72 -2.38 -0.02 1.20 16 52 H 0.05 1.16 6.73 -2.39 -0.02 1.14 16 53 H 0.07 1.28 8.14 -2.38 -0.02 1.26 16 54 H 0.09 1.17 6.91 -2.39 -0.02 1.15 16 55 H 0.07 1.30 8.14 -2.39 -0.02 1.28 16 56 H 0.09 1.16 7.00 -2.39 -0.02 1.14 16 57 H 0.05 1.17 6.61 -2.39 -0.02 1.15 16 58 H 0.06 1.10 6.62 -2.38 -0.02 1.09 16 59 H 0.09 1.06 7.01 -2.39 -0.02 1.04 16 60 H 0.07 1.20 8.14 -2.39 -0.02 1.18 16 61 H 0.18 2.60 8.06 -2.91 -0.02 2.57 16 62 H 0.21 0.92 8.06 -2.91 -0.02 0.89 16 63 H 0.17 2.49 8.06 -2.91 -0.02 2.46 16 Error: len(atom_listwat) != numatom: 63 != 64 `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' cp: cannot stat `output.mol2': No such file or directory /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/372095/xaa-8058088.1' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa' `/scratch/xiaobo/372095/xaa-8058088.1/working' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working' `/scratch/xiaobo/372095/xaa-8058088.1/working/building' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/ZINC001643838682.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/ZINC001643838682.ism' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/ZINC001643838682-numbered.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/ZINC001643838682-numbered.ism' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/input.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/input.ism' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/temp.in-wat' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/ZINC001643838682.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/ZINC001643838682.mol2' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/temp.in-hex' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/fort.19' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/temp.o-hex' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/temp-working.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/temp-working.mol2' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/temp.mol2' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/temp.ZmatMOPAC' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/name.txt' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/fort.21' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/0.mol2.original' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/0.mol2.original' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/temp.o-wat' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/outputwat.log' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/fort.20' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/fort.12' `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/0/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/building/ZINC001643838682/0/outputhex.log' `/scratch/xiaobo/372095/xaa-8058088.1/working/protonate' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/protonate' `/scratch/xiaobo/372095/xaa-8058088.1/working/protonate/xaa-protomers.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/protonate/xaa-protomers.ism' `/scratch/xiaobo/372095/xaa-8058088.1/working/protonate/xaa-protonated-manual.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/protonate/xaa-protonated-manual.ism' `/scratch/xiaobo/372095/xaa-8058088.1/working/protonate/xaa-protomers-expanded.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/protonate/xaa-protomers-expanded.ism' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/906' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/906' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/476' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/476' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/218' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/218' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/491' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/491' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/617' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/617' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/625' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/625' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/707' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/707' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/926' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/926' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/612' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/612' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/197' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/197' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/442' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/442' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/645' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/645' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/575' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/575' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/562' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/562' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/671' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/671' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/756' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/756' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/626' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/626' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/659' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/659' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/634' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/634' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/343' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/343' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/205' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/205' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/405' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/405' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/925' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/925' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/936' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/936' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/895' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/895' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/879' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/879' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/337' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/337' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/706' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/706' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/203' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/203' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/186' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/186' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/1000' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/1000' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/973' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/973' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/628' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/628' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/785' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/785' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/982' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/982' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/968' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/968' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/881' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/881' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/825' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/825' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/550' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/550' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/731' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/731' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/750' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/750' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/115' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/115' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/478' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/478' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/880' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/880' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/301' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/301' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/435' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/435' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/657' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/657' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/826' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/826' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/239' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/239' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/890' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/890' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/624' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/624' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/858' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/858' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/576' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/576' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/834' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/834' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/989' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/989' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/385' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/385' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/887' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/887' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/665' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/665' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/501' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/501' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/686' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/686' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/423' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/423' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/345' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/345' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/883' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/883' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/828' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/828' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/450' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/450' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/255' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/255' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/497' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/497' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/670' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/670' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/282' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/282' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/431' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/431' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/159' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/159' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/430' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/430' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/183' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/183' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/390' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/390' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/764' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/764' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/169' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/169' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/321' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/321' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/529' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/529' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/254' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/254' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/759' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/759' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/636' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/636' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/249' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/249' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/429' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/429' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/113' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/113' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/738' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/738' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/409' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/409' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/656' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/656' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/114' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/114' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/610' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/610' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/369' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/369' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/351' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/351' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/577' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/577' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/120' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/120' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/116' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/116' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/891' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/891' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/316' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/316' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/344' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/344' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/694' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/694' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/174' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/174' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/299' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/299' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/672' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/672' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/164' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/164' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/681' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/681' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/460' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/460' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/586' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/586' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/769' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/769' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/772' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/772' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/145' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/145' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/960' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/960' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/310' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/310' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/537' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/537' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/418' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/418' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/443' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/443' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/184' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/184' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/745' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/745' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/640' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/640' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/638' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/638' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/556' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/556' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/305' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/305' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/683' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/683' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/469' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/469' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/643' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/643' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/735' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/735' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/970' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/970' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/366' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/366' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/315' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/315' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/601' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/601' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/827' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/827' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/729' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/729' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/391' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/391' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/653' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/653' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/323' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/323' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/398' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/398' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/742' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/742' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/784' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/784' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/168' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/168' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/362' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/362' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/440' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/440' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/994' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/994' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/931' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/931' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/861' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/861' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/687' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/687' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/808' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/808' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/182' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/182' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/555' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/555' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/210' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/210' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/286' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/286' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/259' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/259' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/510' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/510' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/782' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/782' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/404' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/404' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/600' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/600' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/313' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/313' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/726' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/726' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/733' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/733' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/458' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/458' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/538' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/538' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/590' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/590' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/240' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/240' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/189' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/189' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/578' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/578' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/824' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/824' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/489' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/489' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/690' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/690' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/652' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/652' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/190' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/190' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/414' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/414' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/781' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/781' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/720' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/720' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/412' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/412' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/718' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/718' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/951' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/951' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/705' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/705' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/910' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/910' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/554' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/554' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/721' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/721' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/847' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/847' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/933' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/933' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/242' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/242' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/932' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/932' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/961' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/961' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/797' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/797' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/288' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/288' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/850' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/850' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/749' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/749' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/214' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/214' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/402' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/402' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/574' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/574' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/644' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/644' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/621' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/621' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/647' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/647' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/521' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/521' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/422' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/422' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/267' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/267' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/452' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/452' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/354' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/354' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/386' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/386' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/532' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/532' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/871' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/871' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/952' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/952' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/901' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/901' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/668' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/668' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/309' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/309' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/370' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/370' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/752' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/752' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/768' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/768' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/277' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/277' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/971' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/971' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/677' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/677' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/716' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/716' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/392' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/392' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/786' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/786' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/319' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/319' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/217' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/217' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/673' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/673' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/263' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/263' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/944' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/944' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/361' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/361' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/553' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/553' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/697' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/697' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/669' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/669' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/999' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/999' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/799' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/799' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/873' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/873' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/481' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/481' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/940' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/940' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/298' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/298' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/454' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/454' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/954' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/954' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/339' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/339' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/635' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/635' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/558' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/558' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/235' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/235' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/126' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/126' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/648' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/648' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/251' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/251' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/195' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/195' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/666' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/666' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/959' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/959' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/253' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/253' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/516' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/516' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/233' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/233' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/929' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/929' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/258' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/258' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/250' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/250' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/948' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/948' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/779' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/779' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/829' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/829' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/817' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/817' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/502' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/502' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/646' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/646' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/767' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/767' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/374' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/374' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/678' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/678' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/661' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/661' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/359' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/359' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/841' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/841' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/388' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/388' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/962' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/962' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/547' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/547' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/322' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/322' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/523' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/523' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/208' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/208' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/496' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/496' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/696' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/696' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/823' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/823' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/930' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/930' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/513' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/513' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/352' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/352' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/761' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/761' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/840' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/840' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/372' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/372' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/888' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/888' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/318' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/318' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/760' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/760' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/279' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/279' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/446' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/446' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/382' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/382' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/146' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/146' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/561' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/561' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/855' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/855' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/350' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/350' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/896' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/896' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/838' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/838' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/219' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/219' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/573' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/573' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/439' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/439' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/902' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/902' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/862' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/862' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/245' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/245' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/447' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/447' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/679' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/679' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/400' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/400' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/358' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/358' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/812' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/812' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/281' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/281' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/534' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/534' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/278' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/278' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/914' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/914' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/213' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/213' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/341' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/341' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/965' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/965' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/306' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/306' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/179' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/179' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/921' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/921' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/938' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/938' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/703' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/703' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/990' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/990' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/471' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/471' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/342' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/342' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/261' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/261' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/297' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/297' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/605' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/605' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/376' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/376' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/568' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/568' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/869' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/869' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/122' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/122' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/585' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/585' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/560' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/560' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/682' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/682' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/790' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/790' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/663' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/663' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/129' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/129' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/244' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/244' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/803' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/803' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/559' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/559' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/176' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/176' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/437' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/437' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/549' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/549' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/143' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/143' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/843' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/843' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/727' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/727' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/783' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/783' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/809' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/809' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/557' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/557' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/854' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/854' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/974' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/974' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/852' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/852' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/234' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/234' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/604' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/604' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/717' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/717' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/142' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/142' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/212' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/212' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/125' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/125' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/517' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/517' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/231' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/231' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/976' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/976' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/816' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/816' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/273' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/273' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/844' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/844' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/163' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/163' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/1001' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/1001' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/592' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/592' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/436' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/436' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/722' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/722' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/228' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/228' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/607' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/607' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/180' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/180' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/444' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/444' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/463' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/463' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/848' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/848' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/256' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/256' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/689' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/689' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/649' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/649' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/715' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/715' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/615' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/615' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/692' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/692' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/916' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/916' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/127' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/127' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/381' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/381' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/997' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/997' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/909' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/909' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/839' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/839' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/851' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/851' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/792' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/792' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/338' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/338' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/490' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/490' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/220' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/220' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/384' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/384' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/530' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/530' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/449' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/449' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/221' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/221' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/271' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/271' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/243' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/243' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/363' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/363' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/699' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/699' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/642' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/642' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/293' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/293' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/571' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/571' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/740' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/740' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/268' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/268' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/832' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/832' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/477' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/477' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/427' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/427' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/704' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/704' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/629' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/629' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/138' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/138' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/599' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/599' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/864' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/864' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/822' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/822' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/631' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/631' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/739' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/739' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/194' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/194' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/533' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/533' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/811' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/811' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/975' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/975' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/751' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/751' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/918' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/918' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/403' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/403' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/762' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/762' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/144' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/144' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/448' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/448' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/913' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/913' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/608' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/608' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/967' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/967' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/124' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/124' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/492' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/492' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/518' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/518' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/885' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/885' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/984' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/984' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/488' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/488' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/257' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/257' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/136' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/136' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/216' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/216' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/468' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/468' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/377' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/377' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/373' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/373' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/831' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/831' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/209' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/209' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/985' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/985' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/702' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/702' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/596' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/596' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/947' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/947' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/655' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/655' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/580' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/580' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/935' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/935' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/712' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/712' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/876' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/876' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/252' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/252' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/581' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/581' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/389' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/389' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/920' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/920' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/801' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/801' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/349' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/349' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/766' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/766' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/329' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/329' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/870' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/870' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/919' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/919' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/152' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/152' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/162' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/162' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/133' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/133' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/773' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/773' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/296' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/296' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/334' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/334' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/526' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/526' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/650' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/650' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/156' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/156' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/232' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/232' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/177' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/177' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/737' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/737' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/332' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/332' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/171' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/171' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/905' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/905' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/466' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/466' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/411' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/411' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/485' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/485' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/587' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/587' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/333' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/333' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/788' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/788' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/484' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/484' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/698' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/698' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/149' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/149' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/191' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/191' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/711' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/711' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/794' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/794' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/241' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/241' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/165' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/165' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/500' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/500' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/204' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/204' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/535' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/535' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/867' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/867' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/922' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/922' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/981' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/981' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/154' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/154' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/364' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/364' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/367' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/367' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/464' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/464' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/520' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/520' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/978' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/978' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/820' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/820' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/303' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/303' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/416' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/416' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/791' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/791' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/417' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/417' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/371' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/371' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/331' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/331' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/651' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/651' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/758' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/758' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/434' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/434' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/957' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/957' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/899' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/899' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/709' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/709' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/977' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/977' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/522' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/522' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/295' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/295' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/723' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/723' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/399' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/399' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/713' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/713' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/741' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/741' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/229' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/229' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/266' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/266' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/356' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/356' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/667' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/667' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/866' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/866' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/969' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/969' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/419' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/419' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/148' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/148' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/215' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/215' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/894' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/894' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/945' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/945' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/525' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/525' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/246' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/246' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/407' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/407' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/453' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/453' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/924' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/924' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/320' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/320' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/583' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/583' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/614' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/614' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/536' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/536' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/597' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/597' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/776' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/776' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/606' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/606' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/821' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/821' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/540' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/540' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/964' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/964' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/591' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/591' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/805' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/805' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/934' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/934' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/360' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/360' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/498' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/498' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/406' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/406' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/357' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/357' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/956' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/956' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/658' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/658' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/849' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/849' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/565' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/565' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/685' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/685' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/178' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/178' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/724' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/724' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/455' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/455' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/462' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/462' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/292' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/292' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/387' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/387' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/247' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/247' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/494' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/494' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/882' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/882' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/346' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/346' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/459' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/459' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/200' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/200' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/958' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/958' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/140' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/140' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/780' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/780' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/482' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/482' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/167' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/167' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/725' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/725' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/856' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/856' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/226' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/226' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/514' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/514' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/995' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/995' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/486' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/486' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/859' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/859' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/396' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/396' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/312' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/312' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/155' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/155' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/433' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/433' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/676' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/676' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/193' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/193' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/582' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/582' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/487' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/487' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/131' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/131' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/814' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/814' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/475' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/475' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/747' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/747' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/774' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/774' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/770' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/770' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/953' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/953' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/813' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/813' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/528' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/528' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/979' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/979' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/917' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/917' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/134' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/134' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/121' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/121' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/753' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/753' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/211' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/211' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/336' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/336' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/701' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/701' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/842' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/842' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/473' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/473' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/294' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/294' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/993' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/993' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/160' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/160' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/746' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/746' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/886' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/886' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/130' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/130' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/511' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/511' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/691' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/691' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/499' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/499' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/566' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/566' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/943' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/943' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/199' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/199' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/889' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/889' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/420' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/420' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/633' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/633' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/264' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/264' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/804' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/804' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/544' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/544' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/508' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/508' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/570' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/570' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/898' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/898' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/542' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/542' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/394' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/394' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/269' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/269' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/465' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/465' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/602' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/602' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/441' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/441' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/274' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/274' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/353' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/353' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/789' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/789' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/236' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/236' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/915' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/915' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/324' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/324' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/410' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/410' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/877' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/877' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/479' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/479' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/907' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/907' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/618' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/618' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/365' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/365' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/355' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/355' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/660' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/660' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/328' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/328' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/765' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/765' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/158' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/158' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/627' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/627' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/325' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/325' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/988' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/988' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/572' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/572' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/470' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/470' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/771' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/771' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/375' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/375' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/280' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/280' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/493' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/493' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/730' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/730' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/137' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/137' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/998' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/998' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/467' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/467' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/845' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/845' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/118' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/118' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/892' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/892' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/451' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/451' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/688' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/688' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/695' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/695' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/763' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/763' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/728' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/728' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/619' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/619' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/238' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/238' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/630' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/630' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/527' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/527' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/777' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/777' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/680' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/680' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/775' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/775' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/793' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/793' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/819' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/819' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/795' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/795' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/939' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/939' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/564' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/564' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/714' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/714' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/980' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/980' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/230' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/230' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/623' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/623' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/265' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/265' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/662' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/662' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/593' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/593' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/290' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/290' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/787' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/787' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/317' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/317' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/552' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/552' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/128' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/128' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/900' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/900' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/991' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/991' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/853' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/853' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/755' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/755' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/818' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/818' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/425' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/425' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/955' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/955' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/594' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/594' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/719' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/719' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/632' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/632' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/166' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/166' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/589' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/589' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/743' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/743' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/472' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/472' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/972' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/972' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/710' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/710' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/579' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/579' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/860' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/860' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/117' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/117' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/911' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/911' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/584' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/584' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/147' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/147' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/289' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/289' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/347' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/347' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/237' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/237' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/674' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/674' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/262' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/262' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/802' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/802' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/161' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/161' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/201' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/201' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/884' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/884' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/260' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/260' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/684' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/684' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/912' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/912' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/272' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/272' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/541' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/541' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/119' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/119' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/595' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/595' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/395' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/395' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/368' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/368' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/157' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/157' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/810' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/810' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/637' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/637' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/588' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/588' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/754' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/754' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/609' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/609' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/173' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/173' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/835' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/835' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/569' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/569' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/378' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/378' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/928' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/928' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/495' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/495' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/865' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/865' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/963' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/963' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/225' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/225' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/181' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/181' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/616' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/616' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/284' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/284' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/830' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/830' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/611' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/611' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/708' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/708' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/545' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/545' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/986' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/986' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/800' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/800' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/807' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/807' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/276' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/276' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/424' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/424' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/139' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/139' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/639' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/639' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/327' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/327' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/141' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/141' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/950' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/950' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/675' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/675' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/815' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/815' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/314' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/314' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/445' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/445' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/744' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/744' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/872' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/872' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/202' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/202' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/432' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/432' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/175' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/175' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/170' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/170' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/457' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/457' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/893' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/893' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/188' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/188' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/330' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/330' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/613' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/613' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/992' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/992' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/248' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/248' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/227' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/227' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/224' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/224' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/806' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/806' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/311' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/311' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/480' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/480' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/304' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/304' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/515' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/515' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/206' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/206' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/509' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/509' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/483' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/483' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/393' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/393' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/937' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/937' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/598' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/598' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/503' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/503' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/563' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/563' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/908' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/908' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/415' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/415' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/302' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/302' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/524' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/524' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/380' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/380' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/946' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/946' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/307' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/307' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/603' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/603' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/551' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/551' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/401' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/401' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/135' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/135' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/983' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/983' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/693' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/693' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/438' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/438' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/505' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/505' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/531' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/531' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/620' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/620' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/664' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/664' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/622' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/622' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/379' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/379' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/878' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/878' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/132' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/132' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/846' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/846' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/335' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/335' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/207' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/207' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/863' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/863' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/942' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/942' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/512' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/512' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/857' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/857' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/196' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/196' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/275' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/275' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/507' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/507' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/736' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/736' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/506' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/506' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/927' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/927' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/421' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/421' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/996' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/996' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/796' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/796' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/287' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/287' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/987' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/987' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/778' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/778' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/283' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/283' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/397' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/397' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/897' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/897' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/798' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/798' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/383' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/383' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/732' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/732' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/874' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/874' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/539' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/539' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/187' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/187' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/300' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/300' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/543' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/543' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/923' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/923' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/836' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/836' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/340' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/340' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/151' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/151' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/150' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/150' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/548' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/548' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/504' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/504' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/546' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/546' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/223' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/223' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/185' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/185' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/308' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/308' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/833' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/833' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/875' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/875' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/757' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/757' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/461' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/461' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/222' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/222' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/426' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/426' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/641' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/641' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/748' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/748' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/904' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/904' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/966' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/966' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/734' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/734' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/198' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/198' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/903' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/903' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/567' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/567' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/172' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/172' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/456' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/456' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/474' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/474' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/700' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/700' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/837' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/837' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/941' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/941' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/654' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/654' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/428' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/428' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/153' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/153' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/291' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/291' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/326' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/326' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/285' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/285' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/408' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/408' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/192' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/192' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/123' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/123' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/270' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/270' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/519' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/519' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/868' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/868' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/348' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/348' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/413' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/413' `/scratch/xiaobo/372095/xaa-8058088.1/working/3D/949' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/3D/949' `/scratch/xiaobo/372095/xaa-8058088.1/working/input-smiles.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/working/input-smiles.ism' `/scratch/xiaobo/372095/xaa-8058088.1/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/finished' `/scratch/xiaobo/372095/xaa-8058088.1/finished/xaa.db2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaa/finished/xaa.db2' removed `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/ZINC001643838682.ism' removed `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/ZINC001643838682-numbered.ism' removed `/scratch/xiaobo/372095/xaa-8058088.1/working/building/ZINC001643838682/input.ism' removed 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